meffil.extract.genotypes: Extract genotype data from PLINK .raw files for Illumina 450K...
In perishky/meffil: Efficient algorithms for DNA methylation
View source: R/extract-genotypes.r
meffil.extract.genotypes R Documentation
Extract genotype data from PLINK .raw files for Illumina 450K SNPs
Description
Extract genotype data from PLINK .raw files for Illumina 450K SNPs
Usage
meffil.extract.genotypes(filenames, verbose = F)
Arguments
filenames
A vector of filenames of PLINK .raw files from which to extract
genotype data.
Value
Matrix with rows corresponding to SNPs, columns to samples and values
equal to 0, 1 or 2 corresponding to genotypes.
Examples
R> writeLines(meffil.snp.names("450k"), con="snp-names.txt")
shell> plink --bfile dataset --extract snp-names.txt --recodeA --out genotypes.raw --noweb
R> filenames <- "genotypes.raw"
R> genotypes <- meffil.extract.genotypes(filenames)
perishky/meffil documentation built on March 20, 2024, 1:56 a.m.
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View source: R/extract-genotypes.r
| meffil.extract.genotypes | R Documentation |
Extract genotype data from PLINK .raw files for Illumina 450K SNPs
Description
Extract genotype data from PLINK .raw files for Illumina 450K SNPs
Usage
meffil.extract.genotypes(filenames, verbose = F)
Arguments
filenames |
A vector of filenames of PLINK .raw files from which to extract genotype data. |
Value
Matrix with rows corresponding to SNPs, columns to samples and values equal to 0, 1 or 2 corresponding to genotypes.
Examples
R> writeLines(meffil.snp.names("450k"), con="snp-names.txt")
shell> plink --bfile dataset --extract snp-names.txt --recodeA --out genotypes.raw --noweb
R> filenames <- "genotypes.raw"
R> genotypes <- meffil.extract.genotypes(filenames)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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